Interpretive Summary: Fatty acids in maize kernels are important for human and livestock health. The identification of genes that improve the balance of fatty acids in maize would allow the quick development of healthier corn via marker assisted selection (MAS). Two genetic mapping techniques designed to identify these genes, linkage mapping and association mapping, were each used to verify the results of the other in one gene identification study. One gene, ZmFatB was confirmed to be able to increase beneficial fatty acids in maize grain by a significant amount. This result was further validated using E. coli bacteria designed to over express the ZmFatB gene that produced much higher levels of beneficial fatty acids than E. coli bacteria without this gene. A simple molecular marker was designed to facilitate its use in MAS for quick production of maize hybrids with high levels of beneficial fatty acids.

Technical Abstract:
Fatty acids in maize kernels are important for human and livestock health. We combined linkage and association analysis to fine-map the major QTL-Pal9 to a 90-kb region, in which only one candidate gene was identified. The gene was named ZmFatB and is orthologous to FatB in Arabidopsis, with a similar gene structure of 6 exons and 5 introns encoding acyl-ACP thioesterase. An 11-bp InDel was found in the last exon of ZmFatB which caused 14 amino acids to differ between the two parents of the QTL mapping population. This is the functional variation of Pal9, controlling the phenotypic variation of palmitic acid content (C16:0) and concentration (C16:0/ALL); the ratio of saturated fatty acids (SFA/ALL); the ratio of unsaturated fatty acids (UFA/ALL); and the ratio of saturated fatty acids to unsaturated fatty acids (SFA/UFA). We used three-dimensional structure analysis of the protein to explain the functional mechanism of ZmFatB, and confirmed the proposed model through gene expression profiling in vivo and E. coli complementary experiments in vitro. We measured the genetic effect of the functional site in different genetic backgrounds, and found a maximum of 4.57mg/g palmitic acid content change accounting for 20~60% of the variation in the ratio of saturated and unsaturated fatty acids. A PCR based marker for QTL-Pal9 was developed using the functional polymorphism for marker-assisted selection (MAS) in maize of the ideal ratio of saturated to unsaturated fatty acids. These findings provide useful insights for understanding the genetic mechanism of oil biosynthesis and targeted maize molecular breeding.